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Title: Numerically Simulating the Hydrodynamic and Water Quality Environment for Migrating Salmon in the Lower Snake River

Abstract

Summer temperatures in the Lower Snake River can be altered by releasing cold waters that originate from deep depths within Dworshak Reservoir. These cold releases are used to lower temperatures in the Clearwater and Lower Snake Rivers, and improve hydrodynamic and water quality conditions for migrating aquatic species. This project monitored the complex three-dimensional hydrodynamic and thermal conditions at the confluence of the Clearwater and Snake Rivers and the processes that led to stratification of Lower Granite Reservoir (LGR) during the late spring, summer, and fall of 2002. Hydrodynamic, water quality, and meteorological conditions around the reservoir were monitored at frequent intervals, and this effort is currently continuing in 2003. Monitoring of the reservoir is a multi-year endeavor, and this report spans only the first year of data collection. In addition to monitoring the LGR environment, a three-dimensional hydrodynamic and water quality model has also been applied. This model uses collected field data as boundary conditions and has been applied to the entire 2002 field season. Numerous data collection sites were within the model domain and serve as both calibration and validation locations for the numerical model. Errors between observed and simulated data vary in magnitude from location to locationmore » and from one time to another. Generally, errors are small and within expected ranges, although model parameters may be improved in the future to minimize differences between observed and simulated values as additional 2003 field data become available. A two-dimensional laterally-averaged hydrodynamic and water quality model was applied to the three reservoirs downstream of LGR (the pools behind Little Goose, Lower Monumental, and Ice Harbor Dams). A two-dimensional model is appropriate for these reservoirs because observed lateral thermal variations during summer and fall 2002 were almost negligible, however vertical thermal variations were quite large (see USACE 2003). The numerical model was applied to each reservoir independently to simulate the time period between May 1 and October 1, 2002. Differences between observed and simulated data were quite small, although improvements to model coefficients may be performed as additional thermal data, collected in the reservoirs during 2003, becomes available.« less

Authors:
; ; ; ; ;
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
15003970
Report Number(s):
PNNL-14297
400480000; TRN: US201015%%254
DOE Contract Number:
AC05-76RL01830
Resource Type:
Technical Report
Country of Publication:
United States
Language:
English
Subject:
13 HYDRO ENERGY; BOUNDARY CONDITIONS; CALIBRATION; DAMS; GRANITES; HYDRODYNAMICS; MONITORING; RIVERS; SALMON; STRATIFICATION; VALIDATION; WATER QUALITY; Lower Snake River; numerical modeling; thermal stratification; salmon; water quality

Citation Formats

Cook, Chris B., Richmond, Marshall C., Coleman, Andre M., Rakowski, Cynthia L., Titzler, P. Scott, and Bleich, Matthew D.. Numerically Simulating the Hydrodynamic and Water Quality Environment for Migrating Salmon in the Lower Snake River. United States: N. p., 2003. Web. doi:10.2172/15003970.
Cook, Chris B., Richmond, Marshall C., Coleman, Andre M., Rakowski, Cynthia L., Titzler, P. Scott, & Bleich, Matthew D.. Numerically Simulating the Hydrodynamic and Water Quality Environment for Migrating Salmon in the Lower Snake River. United States. doi:10.2172/15003970.
Cook, Chris B., Richmond, Marshall C., Coleman, Andre M., Rakowski, Cynthia L., Titzler, P. Scott, and Bleich, Matthew D.. Tue . "Numerically Simulating the Hydrodynamic and Water Quality Environment for Migrating Salmon in the Lower Snake River". United States. doi:10.2172/15003970. https://www.osti.gov/servlets/purl/15003970.
@article{osti_15003970,
title = {Numerically Simulating the Hydrodynamic and Water Quality Environment for Migrating Salmon in the Lower Snake River},
author = {Cook, Chris B. and Richmond, Marshall C. and Coleman, Andre M. and Rakowski, Cynthia L. and Titzler, P. Scott and Bleich, Matthew D.},
abstractNote = {Summer temperatures in the Lower Snake River can be altered by releasing cold waters that originate from deep depths within Dworshak Reservoir. These cold releases are used to lower temperatures in the Clearwater and Lower Snake Rivers, and improve hydrodynamic and water quality conditions for migrating aquatic species. This project monitored the complex three-dimensional hydrodynamic and thermal conditions at the confluence of the Clearwater and Snake Rivers and the processes that led to stratification of Lower Granite Reservoir (LGR) during the late spring, summer, and fall of 2002. Hydrodynamic, water quality, and meteorological conditions around the reservoir were monitored at frequent intervals, and this effort is currently continuing in 2003. Monitoring of the reservoir is a multi-year endeavor, and this report spans only the first year of data collection. In addition to monitoring the LGR environment, a three-dimensional hydrodynamic and water quality model has also been applied. This model uses collected field data as boundary conditions and has been applied to the entire 2002 field season. Numerous data collection sites were within the model domain and serve as both calibration and validation locations for the numerical model. Errors between observed and simulated data vary in magnitude from location to location and from one time to another. Generally, errors are small and within expected ranges, although model parameters may be improved in the future to minimize differences between observed and simulated values as additional 2003 field data become available. A two-dimensional laterally-averaged hydrodynamic and water quality model was applied to the three reservoirs downstream of LGR (the pools behind Little Goose, Lower Monumental, and Ice Harbor Dams). A two-dimensional model is appropriate for these reservoirs because observed lateral thermal variations during summer and fall 2002 were almost negligible, however vertical thermal variations were quite large (see USACE 2003). The numerical model was applied to each reservoir independently to simulate the time period between May 1 and October 1, 2002. Differences between observed and simulated data were quite small, although improvements to model coefficients may be performed as additional thermal data, collected in the reservoirs during 2003, becomes available.},
doi = {10.2172/15003970},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Tue Jun 10 00:00:00 EDT 2003},
month = {Tue Jun 10 00:00:00 EDT 2003}
}

Technical Report:

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  • Summer temperatures in the Lower Snake River can be altered by releasing cold waters that originate from deep depths within Dworshak Reservoir. These cold releases are used to lower temperatures in the Clearwater and Lower Snake Rivers and to improve hydrodynamic and water quality conditions for migrating aquatic species. This project monitored the complex three-dimensional hydrodynamic and thermal conditions at the Clearwater and Snake River confluence and the processes that led to stratification of Lower Granite Reservoir (LGR) during the late spring, summer, and fall of 2002. Hydrodynamic, water quality, and meteorological conditions around the reservoir were monitored at frequentmore » intervals, and this effort is continuing in 2003. Monitoring of the reservoir is a multi-year endeavor, and this report spans only the first year of data collection. In addition to monitoring the LGR environment, a three-dimensional hydrodynamic and water quality model has been applied. This model uses field data as boundary conditions and has been applied to the entire 2002 field season. Numerous data collection sites were within the model domain and serve as both calibration and validation locations for the numerical model. Errors between observed and simulated data varied in magnitude from location to location and from one time to another. Generally, errors were small and within expected ranges, although, as additional 2003 field data becomes available, model parameters may be improved to minimize differences between observed and simulated values. A two-dimensional, laterally-averaged hydrodynamic and water quality model was applied to the three reservoirs downstream of LGR (the pools behind Little Goose, Lower Monumental, and Ice Harbor Dams). A two-dimensional model is appropriate for these reservoirs because observed lateral thermal variations during summer and fall 2002 were almost negligible; however, vertical thermal variations were quite large (see USACE 2003). The numerical model was applied to each reservoir independently to simulate the time period between May 1 and October 1, 2002. Differences between observed and simulated data were small, although improvements to model coefficients may be performed as additional thermal data, collected in the reservoirs during 2003, becomes available.« less
  • Program RealTime provided tracking and forecasting of the 2000 in season outmigration via the internet for stocks of wild PIT-tagged spring/summer chinook salmon. These stocks were ESUs from nineteen release sites above Lower Granite dam, including Bear Valley Creek, Big Creek, Camas Creek (new), Cape Horn Creek, Catherine Creek, Elk Creek, Herd Creek, Imnaha River, Johnson Creek (new), Lake Creek, Loon Creek, Lostine River, Marsh Creek, Minam River, East Fork Salmon River (new), South Fork Salmon River, Secesh River, Sulfur Creek and Valley Creek. Forecasts were also provided for two stocks of hatchery-reared PIT-tagged summer-run sockeye salmon, from Redfish Lakemore » and Alturas Lake (new); for a subpopulation of the PIT-tagged wild Snake River fall subyearling chinook salmon; for all wild Snake River PIT-tagged spring/summer yearling chinook salmon (new) and steelhead trout (new)detected at Lower Granite Dam during the 2000 outmigration. The 2000 RealTime project began making forecasts for combined wild- and hatchery-reared runs-at-large of subyearling and yearling chinook, coho, and sockeye salmon, and steelhead trout migrating to Rock Island and McNary Dams on the mid-Columbia River and the mainstem Columbia River. Due to the new (in 1999-2000) Snake River basin hatchery protocol of releasing unmarked hatchery-reared fish, the RealTime forecasting project no longer makes run-timing forecasts for wild Snake River runs-at-large using FPC passage indices, as it has done for the previous three years (1997-1999). The season-wide measure of Program RealTime performance, the mean absolute difference (MAD) between in-season predictions and true (observed) passage percentiles, improved relative to previous years for nearly all stocks. The average season-wide MAD of all (nineteen) spring/summer yearling chinook salmon ESUs dropped from 5.7% in 1999 to 4.5% in 2000. The 2000 MAD for the hatchery-reared Redfish Lake sockeye salmon ESU was the lowest recorded, at 6.0%, down from 6.7% in 1999. The MAD for the PIT-tagged ESU of wild Snake River fall sub-yearling chinook salmon, after its second season of run-timing forecasting, was 4.7% in 2000 compared to 5.5% in 1999. The high accuracy of season-wide performance in 2000 was largely due to exceptional Program RealTime performance in the last half of the season. Passage predictions from fifteen of the sixteen spring/summer yearling chinook salmon ESUs available for comparison improved in 2000 compared to 1999. The last-half average MAD over all the yearling chinook salmon ESUs was 4.3% in 2000, compared to 6.5% in 1999. Program RealTime 2000 first-half forecasting performance was slightly worse than that of 1999 (MAD = 4.5%), but still comparable to previous years with a MAD equal to 5.1%. Three yearling chinook ESUs showed moderately large (> 10%) MADs. These stocks had larger-than-average recapture percentages in 2000, producing over-predictions early in the season, in a dynamic reminiscent of migration year 1998 (Burgess et al., 1999). The passage distribution of the new stock of hatchery-reared sockeye salmon from Alturas Lake was well-predicted by Program RealTime, based on only two years of historical data (whole-season MAD = 4.3%). The two new run-of-the-river PIT-tagged stocks of wild yearling chinook salmon and steelhead trout were predicted with very good accuracy (whole-season MADs were 4.8% for steelhead trout and 1.7% for yearling chinook salmon), particularly during the last half of the outmigration. First-half steelhead predictions were among the season's worst (MAD = 10.8%), with over-predictions attributable to the largest passage on record of wild PIT-tagged steelhead trout to Lower Granite Dam. The results of RealTime predictions of passage percentiles of combined wild and hatchery-reared salmonids to Rock Island and McNary were mixed. Some of these passage-indexed runs-at-large were predicted with exceptional accuracy (whole-season MADs for coho salmon outmigrating to Rock Island Dam and McNary Dam were, respectively, 0.58% and 1.24%; for yearling chinook to McNary, 0.59%) while others were not forecast well at all (first-half MADs of sockeye salmon migrating to Rock Island and McNary Dams, respectively, were 19.25% and 12.78%). The worst performances for these mid- and mainstem-Columbia River runs-at-large were probably due to large hatchery release disturbing the smoothly accumulating percentages of normal fish passage. The RealTime project used a stock-specific method of upwardly adjusting PIT-tagged smolt counts at Lower Granite Dam. For chinook and sockeye salmon, the project continued using the 1999 formulation for spill-adjustment. For the new stock of wild PIT-tagged steelhead trout, a formula derived for steelhead trout only was used.« less
  • Allowable instantaneous minimum river flows are established in the Columbia and Snake Rivers to ensure safe passage of anadromous fish during their migration to the spawning grounds. However, water storage during periods of low power demands (at night and on weekends) would be beneficial to the power producers. This storage procedure is called ''zero'' river flow and is now permitted on a limited basis when there are few if any actively migrating anadromous fish present in the river system. Requests were made to extend ''zero'' river flow into periods when anadromous fish were actively migrating and a study was initiated.more » Radio-tracking studies were conducted on the Snake River between Lower Monumental and Little Goose Dams to determine the effect of ''zero'' river flow on the migration of adult chinook salmon, Oncorhynchus tshawytscha, and steelhead, Salmo gairdneri. From July through September, 1981, a total of 258 steelhead and 32 chinook salmon were radio-tagged. The rate of migration was used to determine differences between test and control fish and a gamma distribution model was used to describe the migration rate for radio-tagged fish. Estimates of the parameters of the model were used to statistically compare ''zero'' flow and normal river flow conditions for the radio-tagged fish. The results show that the ''zero'' flow condition delays the migration of adult chinook salmon and steelhead; therefore, extended periods of ''zero'' flow to store water are not recommended when fish are actively migrating in the river system. 16 refs., 5 figs., 9 tabs.« less
  • We report results from an ongoing study of survival and travel time of subyearling fall Chinook salmon in the Snake River during 2003 and in the Columbia River during 1999-2002. Earlier years of the study included serial releases of PIT-tagged hatchery subyearling Chinook salmon upstream from Lower Granite Dam, but these were discontinued in 2003. Instead, we estimated survival from a large number of PIT-tagged fish released upstream from Lower Granite Dam to evaluate transportation from Snake River Dams. During late May and early June 2003, 68,572 hatchery-reared subyearling fall Chinook salmon were PIT tagged at Lyons Ferry Hatchery, truckedmore » upstream, acclimated, and released at Couse Creek and Pittsburg Landing in the free-flowing Snake River. We estimated survival for these fish from release to Lower Granite Dam tailrace. In comparison to wild subyearling fall Chinook salmon PIT tagged and released in the free-flowing Snake River, the hatchery fish we released traveled faster and had higher survival to Lower Granite Dam, likely because of their larger size at release. For fish left in the river to migrate we estimated survival from Lower Granite Dam tailrace to McNary Dam tailrace. Each year, a small proportion of fish released are not detected until the following spring. However, the number of fish released in 2003 that overwintered in the river and were detected as they migrated seaward as yearlings in 2004 was small (<1.0%) and had minimal effect on survival estimates. We evaluated a prototype floating PIT-tag detector deployed upstream from Lower Granite reservoir to collect data for use in partitioning travel time and survival between free-flowing and reservoir habitats. The floating detector performed poorly, detecting only 27 PIT tags in 340 h of operation from a targeted release of 68,572; far too few to partition travel time and survival between habitats. We collected river-run subyearling Chinook salmon (mostly wild fish from the Hanford Reach) at McNary Dam, PIT tagged them, and released them to the tailrace as part of an evaluation of transportation from McNary Dam in 2002. Estimated survival in 2002 from the tailrace of McNary Dam to the tailrace of John Day Dam was 0.746 (s.e. 0.036). For migration years 1999-2002, we found that in the reach from McNary to John Day Dam reach, travel time was shorter (migration rate was greater) and survival probabilities were greater when flow volume was greater. Survival was also correlated with water temperature: warmer water was associated with decreased survival, and there was an apparent survival threshold at about 19.3 C (above this temperature survival decreased substantially).« less
  • In 2005, the University of Washington developed a new statistical model to analyze the combined juvenile and adult detection histories of PIT-tagged salmon migrating through the Federal Columbia River Power System (FCRPS). This model, implemented by software Program ROSTER (River-Ocean Survival and Transportation Effects Routine), has been used to estimate survival and transportation effects on large temporal and spatial scales for PIT-tagged hatchery spring and summer Chinook salmon and steelhead released in the Snake River Basin from 1996 to 2003. Those results are reported here. Annual estimates of the smolt-to-adult return ratio (SAR), juvenile inriver survival from Lower Granite tomore » Bonneville, the ocean return probability from Bonneville to Bonneville, and adult upriver survival from Bonneville to Lower Granite are reported. Annual estimates of transport-inriver (T/I) ratios and differential post-Bonneville mortality (D) are reported on both a systemwide basis, incorporating all transport dams analyzed, and a dam-specific basis. Transportation effects are estimated only for dams where at least 5,000 tagged smolts were transported from a given upstream release group. Because few tagged hatchery steelhead were transported in these years, no transportation effects are estimated for steelhead. Performance measures include age-1-ocean adult returns for steelhead, but not for Chinook salmon. Annual estimates of SAR from Lower Granite back to Lower Granite averaged 0.71% with a standard error (SE) of 0.18% for spring Chinook salmon from the Snake River Basin for tagged groups released from 1996 through 2003, omitting age-1-ocean (jack) returns. For summer Chinook salmon from the Snake River Basin, the estimates of annual SAR averaged 1.15% (SE=0.31%). Only for the release years 1999 and 2000 did the Chinook SAR approach the target value of 2%, identified by the NPCC as the minimum SAR necessary for recovery. Annual estimates of SAR for hatchery steelhead from the Snake River Basin averaged 0.45% (SE=0.11%), including age-1-ocean returns, for release years 1996 through 2003. For release years when the ocean return probability from Bonneville back to Bonneville could be estimated (i.e., 1999 through 2003), it was estimated that on average approximately 86% of the total integrated mortality for nontransported, tagged hatchery spring and summer Chinook, and 74% for steelhead, occurred during the ocean life stage (i.e., from Bonneville to Bonneville). This suggests that additional monitoring and research efforts should include the ocean and estuary environment. Annual estimates of the systemwide T/I are weighted averages of the dam-specific T/I ratios for each transport dam (with {ge} 5,000 tagged fish transported), weighted by the probabilities of being transported at each dam. The systemwide T/I compares the observed SAR under the existing transportation system with the expected SAR if the transportation system had not been operated. Estimates of 1.0 indicate that the systemwide transportation program has no effect on SAR, while estimates > 1.0 indicate that the transportation program increases SAR. Excluding the 2001 release group, the geometric mean of the systemwide T/I estimates for hatchery spring Chinook salmon from the Snake River Basin was 1.15 (SE=0.03) for release years 1997 through 2003. The geometric mean of the systemwide T/I estimates for hatchery summer Chinook salmon from the Snake River Basin was 1.28 (SE=0.13) for release years 1997 through 2000 and 2003. Estimates were much higher for the 2001 release groups. These estimates reflect transportation from Lower Granite and/or Little Goose for most release years, depending on the number of tagged smolts actually transported at each dam during each release year. Differential post-Bonneville mortality (D) is the ratio of post-Bonneville survival to Lower Granite Dam of transported fish to that of nontransported ('inriver') fish. Excluding the 2001 release year, the geometric mean of the D estimates for hatchery spring Chinook salmon from the Snake River Basin was 1.00 (SE=0.09) for release years 1997 through 2003. For hatchery summer Chinook salmon from the Snake River Basin, the geometric mean of the D estimates was 1.32 (SE=0.27) for release years 1997 through 2000 and 2003. These estimates reflect transportation from Lower Granite and/or Little Goose, depending on the number of tagged smolts actually transported at each dam during each release year. Approximately half the point estimates of D for both spring and summer Chinook salmon were 1.0 or greater, indicating that for those release groups, transported fish did not have lower ocean and adult survival than nontransported fish. For those years with estimates of D < 1.0, the systemwide T/I estimates were always {ge} 1.0, indicating that despite lower ocean and adult survival of transported fish, transportation did not lower SAR overall.« less